Leading marksman Gary Hooper set up the first after just six minutes with a cross which left Kevan Hurst with a simple tap home at the far post.
Eight minutes later, Hooper struck himself with his 25th goal of the season after crashing a right-foot shot past goalkeeper Owain Fon Williams after an excellent through ball from Henri Lansbury.
It threatened to be a difficult afternoon for Stockport, but they bounced back to reduce the arrears in the 21st minute when centre-back Michael Raynes out-jumped the home defence to head home a free-kick from Michael Rose.
In the second half Stockport tried to force the pace but never really looked like getting an equaliser with Joe Murphy relatively untroubled in the Scunthorpe goal.
It was the home side who went closest to adding to the score with defenders Krystian Pearce and David Mirfin both going close with headers from set-pieces.
Striker Paul Hayes also had a good effort well saved by Fon Williams, who also denied Hooper with another good stop as the game drifted into injury time.
Defeat was a setback for Stockport, who are now losing ground on their bid to snatch a play-off place.
Their young side looked dangerous at set-pieces but they lacked a cutting edge in front of goal against a Scunthorpe defence who have been struggling to keep clean sheets this season.